Significance Recombinant SHIV clones are a means to examine HIV-1 nef gene function in vivo for control of virus load and progression to simian AIDS in rhesus macaques. Novel antiviral therapies and vaccines against HIV-1 Nef could be tested in the SHIVnef monkey model. Objectives An animal model to study both HIV-1 infection and AIDS pathogenesis is not available. To analyze function of specific HIV-1 genes in vivo, SIV/HIV-1 recombinant viruses (designated SHIV) have been constructed by replacing genes in the pathogenic clone SIVmac239 with counterpart HIV-1 genes. We have made SHIV clones containing various HIV-1 nef genes to study nef function in vivo. Results The HIV-1-SF2 and HIV-1-SF33 nef genes were used to replace the nef gene of the SIVmac239 clone. Two juvenile rhesus macaques inoculated with SHIV-SF2nef showed low virus load in the acute stage of infection and in the chronic stage; these animals were healthy for over two years. Two additional juvenile macaques were inoculated with SHIV-SF33nef. One of these animals has maintained low virus load for over two years. In contrast, the second animal showed a rise in virus load at about 6 months and subsequently developed a fatal AIDS-like disease by one year after infection. Virus was recovered from this animal at necropsy and designated SHIV-SF33nefA. Sequence analysis of this virus revealed about 8 amino acid changes in nef relative to the sequence of nef in the input viral clone. Importantly, SHIV-SF33nefA produced a fatal AIDS-like disease in juvenile macaques. Future Directions Intragenic SHIV-SF33nefA recombinants and point mutants, involving the HIV-1-SF33 nef gene, will be constructed to determine which sequence change(s) accounts for viral adaptation and pathogenesis in rhesus macaques. KEY WORDS HIV-1 genes, AIDS pathogenesis, SHIV clones FUNDING NIH Grant AI38532